biocLite() fails to install all limma dependencies from CRAN
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 7.1 years ago
"Gordon K Smyth" <smyth at="" wehi.edu.au=""> writes: > Hi Jenny, > > statmod is deliberately a "suggests" rather than a "depends" because > only a small number of limma functions use it. > > As far I remember, there the Bioconductor install behaviour hasn't > changed. Maybe I misremember, but I don't think biocLite() has ever > installed suggested packages from CRAN. biocLite has not changed its behavior for this release. However, you can use biocLite to install Suggests. Here are a couple ways to do this: biocLite("limma", dependencies=c("Depends", "Suggests", "Imports")) or simply biocLite("limma", dependencies=TRUE) This has one slight downside: install.packages will install the Suggests for all Depends not just the package you asked for. So you can end up getting many more packages than you really need. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
Cancer limma Cancer limma • 3.2k views
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